1-41871577-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024503.5(HIVEP3):​c.-801+46836A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.868 in 152,272 control chromosomes in the GnomAD database, including 57,748 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.87 ( 57748 hom., cov: 33)

Consequence

HIVEP3
NM_024503.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.238
Variant links:
Genes affected
HIVEP3 (HGNC:13561): (HIVEP zinc finger 3) This gene encodes a member of the human immunodeficiency virus type 1 enhancer-binding protein family. Members of this protein family contain multiple zinc finger and acid-rich (ZAS) domains and serine-threonine rich regions. This protein acts as a transcription factor and is able to regulate nuclear factor kappaB-mediated transcription by binding the kappaB motif in target genes. This protein also binds the recombination signal sequence that flanks the V, D, and J regions of immunoglobulin and T-cell receptors. Alternate splicing results in both coding and non-coding transcript variants. [provided by RefSeq, Sep 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HIVEP3NM_024503.5 linkc.-801+46836A>C intron_variant Intron 1 of 8 ENST00000372583.6 NP_078779.2 Q5T1R4-1
HIVEP3NM_001127714.3 linkc.-721+46836A>C intron_variant Intron 1 of 7 NP_001121186.1 Q5T1R4-2
HIVEP3NR_038260.2 linkn.511-22488A>C intron_variant Intron 1 of 2
HIVEP3NR_038261.2 linkn.241-22488A>C intron_variant Intron 2 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HIVEP3ENST00000372583.6 linkc.-801+46836A>C intron_variant Intron 1 of 8 1 NM_024503.5 ENSP00000361664.1 Q5T1R4-1
HIVEP3ENST00000372584.5 linkc.-721+46836A>C intron_variant Intron 1 of 7 1 ENSP00000361665.1 Q5T1R4-2
HIVEP3ENST00000489103.5 linkn.232-22488A>C intron_variant Intron 2 of 3 1
HIVEP3ENST00000491442.5 linkn.258-22488A>C intron_variant Intron 1 of 2 1

Frequencies

GnomAD3 genomes
AF:
0.868
AC:
132127
AN:
152154
Hom.:
57696
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.964
Gnomad AMI
AF:
0.821
Gnomad AMR
AF:
0.813
Gnomad ASJ
AF:
0.847
Gnomad EAS
AF:
0.997
Gnomad SAS
AF:
0.854
Gnomad FIN
AF:
0.826
Gnomad MID
AF:
0.807
Gnomad NFE
AF:
0.823
Gnomad OTH
AF:
0.843
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.868
AC:
132238
AN:
152272
Hom.:
57748
Cov.:
33
AF XY:
0.869
AC XY:
64700
AN XY:
74442
show subpopulations
Gnomad4 AFR
AF:
0.964
Gnomad4 AMR
AF:
0.813
Gnomad4 ASJ
AF:
0.847
Gnomad4 EAS
AF:
0.997
Gnomad4 SAS
AF:
0.853
Gnomad4 FIN
AF:
0.826
Gnomad4 NFE
AF:
0.823
Gnomad4 OTH
AF:
0.845
Alfa
AF:
0.855
Hom.:
6950
Bravo
AF:
0.870

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
2.6
DANN
Benign
0.71

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs710229; hg19: chr1-42337248; API